I lecture Biochemistry at a small University in Oporto. Although originally raised as an experimental Biochemist, I have since changed my research into theoretical and computational chemistry and biochemistry. In this blog, I will mostly commment on recent (or not so recent...) research papers that happen to have called my attention. I hope someone will find it interesting/useful :-)

Thursday, August 30, 2012

Protein synthesis is nowadays achieved through molecular biology techniques: the relevant gene is cloned in an appropriate vector, over-expressed with e.g. a poly-histidine tag, and then purified through high affinity chromatography. Peptide chemistry is therefore often forgotten by biochemists, unless we need to order a short customized peptide from a commercial source. Danishefsky et al. have now combined solid phase peptide synthesis, native chemical ligation and metal-free dethyilation to synthesize a number of analogues of human parathormone. Their strategy afforded native parathormone with higher purity than obtained from commercial sources, as well as pure analogues not achievable by any other means. These analogues were shown to be much more stable (10% decomposition in 7 days) than parathormone ,(>90% loss in 7 days), and to be as active as parathormone when injected to mice.
This is a very interesting work, which should pave the way towards the synthesis of long-lived synthetic peptide hormones, thus potentially decreasing the number of injections needed to control hormone levels in patients suffering from impaired endocrine function.

Friday, April 13, 2012

Drawing complex three-dimensional molecules in two-dimensions can be a real torture. I am glad I have never had to draw anything as convoluted as palhinine A. Check the 3-D structure on the left, and try to draw it in less than 10 minutes in ChemDraw or ChemSketch. Good luck!

Thursday, March 15, 2012

How large must a quantum model of an enzyme active site be to achieve optimum results? Proponents of the so-called "cluster model" argue that, most often, good results may be obtained even with small models (&lt 100 atoms). Fahmi Himo hasrepeatedly shown that fully including the first layer of aminoacids surrounding the reacting substrate (i.e. to about 150 atoms) yields results that are insensitive to the inclusion of a polarizable-continuum solvent field, and has concluded from these data that such models are sufficient to capture all the relevant enzymatic effexts on catalysis.

Walter Thiel has now published a QM/MM analysis of the reaction mechanism of acetylene hydratase (previously studied by Fahmi Himo using increasingly large QM-only models). Inclusion of the surrounding protein dramatically changed the results for the largest model studied by Himo, due to the absence (in the "cluster model") of two negatively charged phosphate groups adjacent to the active site. Although these charges are quite "shielded" from the active site because of neighbouring positively-charged amino acids, they originate local charge assymmetries that interact differently with the active site during each step of the catalytic cycle. This effect is quite similar to the major influence of the internal protein dipoles on enzyme catalysis expounded by Arieh Warshel, and should be kept in mind by all of us who tend to prefer the QM-only approach: a polarizable-continuum model assumes a homogeneous environment surrounding the QM system, and in proteins "it ain't necessarily so".